Work on ResidualVM, just like any other volunteer-based Open Source project depends largely on the motivation and spare time of the volunteers involved, which means that there are periods of high activity, and periods of lower activity.

As for your issue, no one has gotten around to fixing that yet, the preferable way to get sure it gets solved at some point, is to do as Botje asked, and file a bug ticket on Github about the issue, then when someone decides to use some of their spare time to work on EFMI-related stuff in ResidualVM, they might fix that bug, as from the looks of it, it shouldn't be _too_ complicated to fix.

I just closed this issue as I found out it's not actually a bug. The menu controllers are always default upon loading the game. However, when you load your saved game, it will also load your custom controller settings.